Data Releases 2024

8 April 2024

FinnGen EA3 OCT data (of EA3 AMD project) and ECG data (of EA3 Heart Failure project)

These are pilot data sets for new data types planned for FinnGen 3.

Optical coherence tomography (OCT) images for AMD patients are acquired from Eastern Finland Biobank. Data set contains longitudinal OCT images and corresponding dates.

ECG pilot data is from Cental Finland biobank and contains longitudinal ECGs from all individuals from whom ECG has been taken.

• /finngen/library-red/EA3_AMD_2.0/

• /finngen/library-red/EA3_HEART_FAILURE_1.0/

13 March 2024

FinnGen NMR data

NMR data of FinnGen samples provided to THL from Nightingale which is now released to the FinnGen Sandbox for analysis.

This data contains 46,556 samples from the following THL BIOBANK cohorts:

DILGOM2007 n= 4539 DILGOM2014 n= 1186 FINRISK1997 n= 7095 FINRISK2002 n= 6968 FINRISK2007 n= 5299 FINRISK2012 n= 5440 FinHealth17 n= 5165 Health2000 n= 6574 Health2011 n= 4290

Number of samples: (46556) Number of unique FinnGen IDs: (37245) Number of FinnGen IDs that occur more than once: (8149) Number of NMR variables: (between 330 and 494)

There are 330-494 NMR variables which are further described in Variable_description *.csv files

All data has been consistently analyzed by Nightingale with their latest software and is described in detail in the manuscript available at https://www.medrxiv.org/content/10.1101/2023.06.09.23291213v1

Note that many of the samples are taken on the same individuals at different time points (e.g., Health2011 is a followup of Health2000, and DILGOM2014 is likewise followup of DILGOM2007 (a subset of FINRISK2007) - in total there are 8,149 repeated samples. Hence the sample size for genetic association is more on the order of 35,000 but there are very valuable longitudinal analyses possible.

• /finngen/library-red/nmr/

28 February 2024

FinnGen WES gnomAD v4 vcf files

This data release contains 25,201 samples in total from the FINRISK (n=12203), Health2000 (n=4618) and SUPER (n=8380) collections. The sample is highly enriched for psychosis patients (the entire SUPER cohort) and subsets of FINRISK were selected as part of Alzheimer's and IBD sequencing projects.

These data were extracted from the gnomAD v4 exome callset generated at the Broad Institute and have not gone through additional QC after the gnomAD calling.

• /finngen/library-red/wes_gnomad_v4_no_qc/

20 February 2024

FinnGen WGS Gnomad v3 vcf files. This data contains 2,463 samples from FINRISK, H2000, Migraine and SUPER cohorts. The data has not gone through any QC.

• /finngen/library-red/wgs_gnomad_v3_no_qc/

9 February 2024

Pathology data of FinnGen EA3 Oncology - Ovarian Cancer project

• /finngen/library-red/EA3_CANCER_OVARIAN_1.0/

FinnGen WGS SISu v4 vcf files. This data contains 3,237 FINRISK samples and has not gone through any QC.

• /finngen/library-red/wgs_sisu_v4_no_qc/

7 February 2024 FinnGen Genetic Ancestry data

• /finngen/library-red/finngen_R12/genetic_ancestry_1.0

1 February 2024

FinnGen EA3 prostate cancer pathology data

• /finngen/library-red/EA3_CANCER_PROSTATE_1.0/

17 January 2024

Added data for physiological measurements for EA3 Women's health PCOS project

• /finngen/library-red/EA3_WOMENS_HEALTH_PCOS_1.0/

16 January 2024

Updated version of FinnGen DF12 mosaic chromosomal alterations data. The main change is that the previous release (mca_1.1) used SHAPEIT5 for phasing while the updated release (mca_2.1) changed back to SHAPEIT4.

• /finngen/library-red/finngen_R12/mca_2.1/

10 January 2024

Added age group information for FinnGen EA3 Women's health PCOS project

• /finngen/library-red/EA3_WOMENS_HEALTH_PCOS_1.0/